Background In the past decade, a strong argument has been built for the role of serotonin (5HT) and the serotonin transporter (SERT) in irritable bowel syndrome (IBS). However, it is still not clear how SERT contributes to this clinically heterogeneous disease. The present study addressed this issue by implementing platelet (plt) markers of SERT activity in the assessment protocol. Methods Fasting blood samples of 149 (51 male/98 female) subjects with Rome II and III defined IBS subtypes, and 163 healthy control subjects (CSs; 75 male/88 female) were analyzed for platelet 5HT concentration and 5HT uptake activity maximum uptake rate (V max) and affinity constant (K m). Results Gender had a significant impact on platelet markers of SERT activity. Male IBS patients showed significantly lower median V max and K m values than the male CS (V max 1.706 vs. 2.148 nmol/10⁹ plts × min, P < 0.001; K m 346 vs. 410 nmol, P = 0.008) without any significant reduction in platelet 5HT concentration (362 vs. 394 ng/10⁹ plts). On the other hand, V max values were not different between female IBS patients and female CS (1.642 vs. 1.741 nmol/10⁹ plts × min), but platelet 5HT concentration was significantly lower in females with diarrhea-predominant IBS (363 vs. 435 ng/10⁹ plts, P < 0.05). Conclusion Although an absolute extrapolation from platelets to the gastrointestinal tissue does not appear to be justified, our findings demonstrated that the contribution of disturbed SERT activity to IBS is not uniform and is possibly gender-specific. The results suggest that an assessment of SERT function in platelets may help to elucidate the differences between IBS patients in response to drugs affecting the 5HT system.