In this study, we aimed to make a comparison between chromosomal effects caused by conventional phototherapy and intensive phototherapy in jaundiced newborns. The study group included 83 newborns with gestation age of > or =35 weeks, and on days 3-10 after birth. Newborns were divided into four groups on the basis of total serum bilirubin (TSB) levels upon admission and need for phototherapy. The intensive group (n=19) consisted of newborns who received light-emitting diode (LED) phototherapy, the conventional group (n=23) consisted of newborns who received conventional phototherapy, the jaundiced control group (n=21) consisted of newborns whose TSB levels were higher than 10mg/dL (average = 13.7 + /-1.5 mg/dL) on admission and who did not receive phototherapy, and the non-jaundiced control group (n=20) consisted of newborns whose TSB levels were less than 5 mg/dl (average = 3.6 +/- 0.8 mg/dL). TSB level of the intensive group at admission was 20.2 +/- 1.3 mg/dL, whereas the level of conventional group was 19.6 +/- 1.5 mg/dL. Blood samples were taken from all infants on admission to determine sister chromatid exchange (SCE1) frequency. Blood sampling was repeated on discharge (SCE2) of infants who had received phototherapy. Demographic information, hospitalization details and the rate of decline in TSB were recorded, and frequencies of SCE1 and SCE2 were compared. There was no difference in demographic information among the four groups. SCE1 frequencies in 50 metaphases were evaluated in the intensive, conventional, jaundiced control and non-jaundiced control groups, and the SCE1 frequency was determined as 9.37/cell, 9.54/cell, 9.23/cell and 6.17/cell, respectively. The SCE1 frequency of the jaundiced groups (intensive, conventional and newborns-with-jaundice control group) was significantly higher than that in the non-jaundiced control group (p = 0.001). There was no significant difference between the intensive group and the conventional group in SCE2 frequency (13.5/cell vs. 13.55/cell, p = 0.39). SCE2 frequency was higher than SCE1 frequency in both the intensive and conventional groups (p = 0.001). A strong correlation was found between admission TSB and SCE1 frequency (p = 0.001; r = 0.79). The rate of decline in TSB was higher in the intensive group compared with the conventional group (0.26mg/(dLh) vs. 0.14 mg/(dLh); p = 0.001). We found that intensive and conventional phototherapies similarly increase SCE frequency in newborns. There was a strong, positive correlation between the TSB-on-admission level and SCE1 frequency. In the light of this study, we may conclude that intensive and conventional phototherapies may have an effect on chromosomes in jaundiced newborns. TSB levels higher than 10mg/dL are, too, reported hazardous on chromosomes. Further studies are warranted to elucidate this relationship.