Although an undescended testes (UDT) is the most common developmental anomaly of the urogenital organ in males, they have often been regarded as mild malformation and as a consequence have been poorly reported despite its association with increased risk of infertility and testicular cancer in later life. In Nigeria, data on its prevalence is scarce. The objective of the study was to determine the prevalence rates of undescended testes at birth, 3 months and 6 months of age respectively. A prospective hospital-based cohort study was conducted to determine the prevalence rates of UDT at birth, 3 months and 6 months of age. The infants were examined at birth for UDT, using standardized technique. The infants who were identified at birth to have undescended testes were re-examined at the ages of 3 and 6 months respectively. To minimize inter-observer error, one physician examined all the infants. The gestational age, birth weight and birth position of each the neonates were recorded. The maternal age, parity, educational attainment and occupation of the parents were noted. The season in which each of the infants was born was recorded. At birth, 2.8% (39 of 1,394) of live-born male infants had undescended testes (UDT). This prevalence rate declined to 1.2% at the age of 3 months and 0.6% at the age of 6 months with an overall spontaneous testicular descent rate of 79.5% (31 of 39 cases). The prevalence rates were significantly elevated for low birth weight and preterm infants. The frequency of spontaneous descent of the testes was higher in both low birth weight and preterm infants compared to normal birth weight and full-term infants respectively. Comparing twin and non-twin infants, the prevalence of UDT was 3.8% (2 of 52) versus 2.8% (37 of 1,342); p>0.05. At birth, low birth weight and preterm infants had a significantly higher prevalence than their full-term as well as preterm counterparts with preterm infants having a greater tendency to achieve spontaneous descent of the testicles than full-term infants.