Congenital cytomegalovirus (cCMV) infection is the leading non-genetic cause of long-term neurological and sensory sequelae, the most common being sensorineural hearing loss (SNHL). Standard therapy for infants with symptomatic cCMV is valganciclovir for six months. However, little is known about the effects of antiviral therapy on CMV diversity while patients are on treatment. In this study, CMV variation was analyzed from urine specimens isolated from two patients with cCMV shortly after birth and at seven months. One was treated with valganciclovir for six weeks and the other for six months. In order to track these variants a novel bioinformatic approach was employed to analyze changes in low frequency variants over time. In the infant receiving antivirals for only six weeks, there was a fourfold increase in variation in UL97 from the seven month specimen. Furthermore, an eightfold increase in variation was seen in UL83 (pp65) with seven potential escape mutations occurring, and a twofold increase in UL73 (gN). In contrast variation did not increase or was reduced in these coding regions in the infant receiving valganciclovir for six months. However, there were increases in other CMV regions in samples isolated from both patients indicating further longitudinal studies are warranted to better understand the interplay between CMV diversity, antiviral therapy and patient outcome.