In this study, we aimed to clarify the following questions: 1) Does phototherapy (PT) cause genotoxicity in full-term newborn babies undergoing PT as a result of neonatal jaundice?, 2) if genotoxic effect occurs, is there any relationship between the duration of PT and genotoxicity?, and 3) is genotoxic effect temporary or not? The frequency of sister chromatid exchange (SCE) was determined in jaundiced newborns before, during, and after phototherapy, then determined again in childhood (approximately 3.5 years old). Mean frequency of SCE of 22 full-term jaundiced babies significantly increased during the PT procedure and in every single day, compared to the previous day, in comparison to the pre-PT basal value (6.20 ± 0.57;); mean SCE frequencies at 24, 48, 72, and 96 hours were 7.75 ± 0.40, 8.16 ± 0.47, 8.50 ± 0.40, and 9.36 ± 0.55, respectively (all P-values <0.01). In childhood, no significant difference was found between the mean SCE value (4.9 ± 0.9) of 20 of 22 children, who received PT in the neonatal period, and the mean SCE value (4.7 ± 0.6) of 20 coevaluated healthy children (P = 0.40). This study demonstrates that the negative effect of PT on SCE is a temporary effect.