Background and Objectives: Phototherapy is one of the most common and invasive methods in treatment of unconjugated hyperbilirubinemia of the neonate. Adverse effects of phototherapy include loose stools, skin rash and dehydration. There are very few studies which show the effect of phototherapy on total count and reticulocyte count. So, this study was done to show the effect of phototherapy on total count and reticulocyte count. Subjects and Methods: This is a prospective hospital based comparative study  on 100 eligible neonates admitted in the Neonatal Intensive Care Unit receiving phototherapy at Adichunchanagiri Institute of Medical Sciences and research hospital, a rural tertiary care hospital, B.G.Nagara, Nagamangala Taluk, Karnataka from December 1st 2013- November 30th 2014. Two samples before and after phototherapy, were taken and analysis was done. The results were analysed statistically. Results:   A total of 100 neonates were included in our study of which 55(55%) were males and 45(45%) were females. The mean(+/-SD) total countwas 15463.5+/-163.6 before phototherapy and 15363+/-151.83 after phototherapy.   The mean(+/-SD) reticulocyte count was 3.07+/-0.13% before phototherapy and 2.79+/-0.10%  after phototherapy.  Conclusion: In our study phototherapy has a significant effect on reticulocyte where as there was no significant effect on total count including neutrophils and leucocytes.