Is Your Paper Ready for IJMS? Understanding MDPI's Largest Molecular Sciences Journal

This is where IJMS gets interesting, and where you need to pay attention. A large fraction of IJMS publications come through special issues, thematic collections organized by guest editors who invite submissions on specific topics. MDPI runs hundreds of these across its journals at any given time, and IJMS is no exception.

Here's what that means for you as an author. If you submit to a regular issue, your paper goes through the standard editorial pipeline: an academic editor handles it, sends it to reviewers, and makes a decision. If you submit to a special issue, a guest editor manages the process. That guest editor is typically a researcher in your subfield who has agreed to organize the collection and recruit papers.

Neither route is inherently better or worse, but they aren't identical either. Special issues can offer faster processing because the guest editor is motivated to fill the collection. They can also connect you with a handling editor who genuinely understands your subfield, which matters when your paper sits at the intersection of, say, molecular pharmacology and computational chemistry. On the other hand, some special issues have been criticized for lower selectivity. If a guest editor needs to fill 30 slots and has received 35 submissions, the acceptance dynamics aren't the same as a regular issue where there's no quota pressure.

My advice: don't treat special issues as an easier path. Submit to one if the topic genuinely matches your work and the guest editor's expertise adds value. If you're getting cold emails inviting you to submit to a special issue on a topic that only vaguely relates to your research, that's a signal to be cautious. The best IJMS special issues are tightly themed and well-curated. The worst ones are grab bags that dilute the journal's reputation.

Even with a 40-50% acceptance rate, IJMS doesn't publish everything. Here are the patterns I've seen in papers that don't make it past the first screen.

Out-of-scope submissions. IJMS is broad, but it isn't unlimited. Pure clinical trials without a molecular component won't fit. Engineering papers without molecular-level investigation won't fit. Ecology papers won't fit. If your work doesn't have a clear molecular angle, you're wasting your time and the editor's.

Missing or fabricated data red flags. MDPI has invested in integrity screening tools, and IJMS uses them. If your images look manipulated, if your gels have suspicious splicing, or if your numerical data doesn't pass basic statistical consistency checks, the paper will be flagged before it reaches review. This isn't unique to IJMS, but the journal has gotten more aggressive about it in recent years.

Papers that are actually conference abstracts. IJMS gets submissions that read like extended abstracts, thin methods, minimal results, and a discussion that's two paragraphs of speculation. A 3,000-word paper with one figure and a lot of hand-waving won't survive triage. You don't need to write a 15,000-word monograph, but the work needs to be complete.

Duplicate or salami-sliced work. If you've already published the same dataset in another journal and you're trying to squeeze a second paper out of it by changing the framing, IJMS editors will catch it. MDPI runs similarity checks on all submissions, and recycled text triggers immediate scrutiny.

No ethics approvals. Human subjects research without IRB/ethics committee documentation, animal studies without IACUC protocols, these are non-starters. IJMS checks, and missing documentation means automatic rejection.

Researchers considering IJMS are often weighing it against a handful of other broad-scope molecular journals. Here's how they compare.

A few things stand out from this comparison. If your paper is primarily about chemical synthesis or molecular characterization without a strong biological component, Molecules might be a tighter fit than IJMS. If it's squarely about cell biology, Cells could work better. Both are MDPI journals with similar review processes, so the operational experience won't differ much.

International Journal of Biological Macromolecules is an Elsevier journal with a higher IF and narrower scope. If your work focuses on proteins, polysaccharides, nucleic acids, or other macromolecules, it's worth considering, but it's more selective and slower.

Scientific Reports is the comparison that comes up most often. It's published by Springer Nature, which carries different brand associations than MDPI. The IF is lower than IJMS, but some researchers feel more comfortable with the Springer Nature label. That's a perception issue, not a quality issue. Both journals are indexed in the same databases. Both are legitimate. But if you're in a department where colleagues raise eyebrows at MDPI, that perception matters for your career whether it should or not.

Let's talk about it directly, because you're thinking about it. MDPI has a reputation problem in parts of academia. Some researchers view it as a predatory or borderline publisher. Others see it as a legitimate open-access operation that's simply grown very fast. The truth is somewhere in the middle, and it depends on which MDPI journal you're looking at.

Here's what's objectively true about MDPI and IJMS specifically. MDPI is based in Basel, Switzerland. It publishes over 400 journals. It's listed in DOAJ. IJMS is indexed in Web of Science, Scopus, and PubMed. It has a real impact factor calculated by Clarivate. Papers published in IJMS get cited, and those citations count in every metric system that matters for tenure and promotion.

Here's what's also true. MDPI's growth model involves publishing enormous volumes across many journals. Some of its journals have faced criticism for rapid acceptance, aggressive email solicitation for special issues, and editorial boards that don't always exercise strong oversight. The sheer number of special issues has led to concerns that some collections exist primarily to generate APC revenue rather than to advance a coherent research theme.

Does this apply to IJMS? Not uniformly. IJMS is one of MDPI's flagship journals. It has a real editorial board, a real impact factor, and a real citation record. But it's also one of the highest-volume journals in the world, and that volume inevitably means variation in quality. You'll find excellent papers in IJMS, and you'll find mediocre ones. That's true of most high-volume journals, including Scientific Reports and PLOS ONE.

My honest take: if a hiring committee or tenure review board at your institution views MDPI negatively, that's a real career consideration and you shouldn't ignore it. It doesn't matter whether the criticism is fair. What matters is whether publishing in IJMS will help or hurt you in your specific professional context. If you're a postdoc applying for faculty positions at institutions that are skeptical of MDPI, you might want to target a different journal even if IJMS would accept your paper. If you're an established researcher who needs to get solid work published quickly and isn't worried about brand politics, IJMS is a perfectly reasonable choice.

IJMS isn't always the best option, but there are situations where it makes clear sense.

You need speed. If your research is time-sensitive, maybe someone else is working on the same problem, or your results are relevant to a current public health situation, IJMS's 2-4 week review cycle and 6-10 week total publication timeline are hard to beat. Most traditional journals can't match that turnaround.

Your paper is solid but not flashy. You've done a careful study, the data are clean, and the conclusions are justified. But there's no dramatic finding that would excite an editor at a high-profile specialty journal. IJMS will evaluate the work on its technical merits without asking whether it'll make the news.

You want open access without the Nature Communications price tag. At $2,900, IJMS isn't cheap, but it's less than half what you'd pay at many Nature-branded journals. For labs with limited publication budgets, that difference matters. And MDPI does offer institutional discounts and occasional waivers.

You're building a publication record in a new area. If you've moved into a new research direction and don't yet have the track record to publish in the top specialty journal for that field, IJMS can be a reasonable place to establish your work while building toward more selective targets.

The special issue topic is perfect. When a well-organized special issue aligns precisely with your research, the combination of a knowledgeable guest editor and a targeted readership can actually give your paper more visibility than a regular issue submission to a similar journal.

Before you submit, it's worth running your manuscript through a free AI manuscript review to check for the kinds of issues that trigger desk rejection anywhere, missing methods details, conclusions that overreach, statistical problems. IJMS reviews quickly, but there's no reason to waste even two weeks on a preventable rejection.