Male reproductive performance has more impact on overall herd productivity than in the female. In order to assess herd productivity in cattle in Nyagatare, Eastern Rwanda, the proportional distribution of male reproductive organ abnormalities was investigated in 3087 bulls slaughtered over a 4-year period. The aim of the study was to investigate the proportional distribution of male reproductive organ abnormalities in exotic and indigenous bulls slaughtered over a 4-year period at Nyagatare abattoir in Eastern Rwanda. Positioning of the testicles was observed and recorded as the animals were assembled before slaughter. After slaughter, the internal and external reproductive organs of all bulls were removed, labelled and analysed for pathology. Significantly more indigenous (79.01%) than exotic (20.99%) animals were slaughtered (P < 0.05; N = 3 087). Overall occurrence of abnormalities was significantly higher in exotic (20.83%) than in indigenous (10.33%) animals (P < 0.05). Overall, abnormal location of testicles was the most common abnormality (4.08%) followed by abnormal prepuce and penis (2.33%), orchitis (1.94%), enlarged vesicular gland (0.91%), scrotal hernia (0.87%), unilateral cryptorchidism (0.81%), testicular hypoplasia (0.81%) and hydrocoele (0.78%). Abnormal location of testicles, abnormal prepuce and penis, orchitis, testicular hypoplasia and enlarged vesicular glands had significantly higher prevalence in exotic animals than in indigenous animals (P < 0.05). There was no significant difference in the prevalence of unilateral cryptorchidism, hydrocoele and scrotal hernia between the exotic and indigenous breeds. The encountered reproductive abnormalities result in poor herd fertility manifesting as low first-service conception rates, prolonged breeding seasons and reduced weaning weights accompanied by inevitable financial losses in beef production. The observed high proportion of male reproductive abnormalities in exotic breeds might offset the professed benefits from introduction of these exotic breeds with the aim of improving productivity.