In fact, that’s not as likely as you might think it is.
When the editor surfaces, emerges from the shadows, and sends you the decision email, it’s most likely to say that your article can be “accepted with (minor or major) revisions”. You’ll have to reply to each of the peer review comments and resubmit a revised manuscript that complies with some or most of the reviewers’ and editor’s suggestions or requests. In my opinion, the revised manuscript is usually improved in the process.
If the editor says that your manuscript cannot be accepted, then it is usually because it’s not within the aims and scope of the journal or not targeted to the journal’s readers. You can avoid this misstep by visiting the journal’s Internet site to identify the target audience, determine the aims and scope, and take a look at prior publications. Before submitting, be sure that you’ve complied with the author guidelines for length and for formatting the text, references, figures, and tables.
There are few other things that you can do to ensure the best responses from the reviewers and your assigned editor. Review the text carefully to be sure that it clearly expresses your intended meaning. Correct any spelling and grammar errors. Make sure that abbreviations and acronyms are spelled out at first use in the Abstract and again in the body of the manuscript, especially if some are not standard abbreviations.
Look for, and correct, any inconsistencies in the presentation of data in the text, tables, and figures, as well as the technical or experimental terms and units that you use. Be sure that the description in Materials and Methods of what you did corresponds to the description in Results of what you found.
Be sure that you have completely described your statistical methods and how you used them, as that might anticipate any questions about the conclusions that you’ve drawn. The Editor-in-Chief is usually responsible for maintaining the journal’s profile and scope, and often has the final say on content. Therefore, check that the Discussion includes mention of what is novel about your research and/or how it adds to what is already known. Journals often ask for the names of potential reviewers, but generally don’t want the names of people that you’ve collaborated with. If you have trusted colleagues or friends who can’t be reviewers, you might ask one or more of them for a pre-peer review of your manuscript.
It seems that most of you do choose journals that are likely to accept your article for publication. The authors of a recent publication (Calcagno et al., Science 2012;338:1065–69) followed the path from submission to acceptance of over 80,000 papers submitted to 923 biology journals between 2006 and 2008.
They found that about 75% were eventually published by the first journal that they were sent to, and those that went through one or more rounds of revision prior to final acceptance were cited more often than papers that were accepted without change. So, if you do your homework and get that manuscript off your desk, then you’re likely to be rewarded with suggestions for revisions that will improve your paper, “catch the eye” of readers, and be often cited. Hey—it’s better to be an optimist (or even a realist) than a pessimist, isn’t it?