Differences in moral sentiments are widespread. Increasingly, their biological correlates are investigated to elucidate potential sources of divergent moral attitudes and choices. Serotonin is one such potential modulator. We investigated the effects of a functional serotonergic polymorphism, 5-HTTLPR, which was previously linked to moral choices albeit with inconsistent findings. N = 157 healthy young adults completed a set of congruent and incongruent moral dilemmas. In addition to the traditional moral response score, this set allows by using a process dissociation (PD) approach an estimation a deontological and a utilitarian parameter. While there was no main effect of 5-HTTLPR on any of the three moral judgement parameters, there was an interaction effect between 5-HTTLPR and endocrine status on PD parameters, which was mainly due to the deontological but not the utilitarian parameter. In men and free cycling women, LL homozygotes showed reduced deontological tendencies compared to S allele carriers. Contrariwise, in women using oral contraceptives, LL homozygotes had increased deontology parameter scores. Furthermore, LL genotypes in general reported less difficulty in making harmful choices, which were in addition associated with less negative emotions. The findings suggest that 5-HTTLPR might be involved in modulating cognitive and emotional processes contributing to moral decisions.