Background The effect that sponsorship has on publication rates or overall effect estimates in animal studies is unclear, though methodological biases are prevalent in animal studies of statins and there may be differences in efficacy estimates between industry and non-industry sponsored studies. In the present analysis, we evaluated the impact of funding source on publication bias in animal studies estimating the effect of statins on atherosclerosis and bone outcomes. Methods We conducted two independent systematic reviews and meta-analyses identifying animal studies evaluating the effect of statins on reducing the risk of atherosclerosis outcomes (n = 49) and increasing the likelihood of beneficial bone outcomes (n = 45). After stratifying the included studies within each systematic review by funding source, three separate analyses were employed to assess publication bias in these meta-analyses—funnel plots, Egger’s Linear Regression, and the Trim and Fill methods. Results We found potential evidence of publication bias, primarily in non-industry sponsored studies. In all 3 assessments of publication bias, we found evidence of publication bias in non-industry sponsored studies, while in industry-sponsored studies publication bias was not evident in funnel plots and Egger’s regression tests. We also found that inadequate reporting of sponsorship in animal studies is still exceedingly common. Conclusions In meta-analyses assessing the effects of statins on atherosclerosis and bone outcomes in animal studies, we found evidence of publication bias, though small numbers of industry-sponsored studies limit the interpretation of the trim-and-fill results. This publication bias is more prominent in non-industry sponsored studies. Industry and non-industry funded researchers may have different incentives for publication. Industry may have a financial interest to publish all preclinical animal studies to maximize the success of subsequent trials in humans, whereas non-industry funded academics may prefer to publish high impact statistically significant results only. Differences in previously published effect estimates between industry- and non-industry sponsored animal studies may be partially explained by publication bias. Electronic supplementary material The online version of this article (doi:10.1186/s12874-015-0008-z) contains supplementary material, which is available to authorized users.