Introduction: Successful strategy for bowel preparation (prep) for colonoscopy aims at administering small–volume oral cathartics coupled with restricted solid food intake. An effective, safe, and standardized bowel preparation in children that is easily administered and acceptable has not yet been determined for children undergoing colonoscopy. Methods: This study compared the efficacy and acceptability of oral sodium phosphate (NaP) regimen 1 day prior to the examination at 1 mL/kg/day with a maximum 90 mL (2/3 dose in the morning, a maximum 45 mL, the remainder in the evening) (regimen A) to our standard prep regimen magnesium citrate 4 mL/kg/day in the morning (maximum 240 mL) for 3 days prior to, and a NaP enema the morning of the colonoscopy (regimen B). Both groups were only allowed clear liquids on prep days and nothing by mouth after midnight. After informed consent, 45 children (22 females) were randomized. Weight, vital signs, electrolytes, calcium, phosphorus and magnesium were taken at screening and on the day of the colonoscopy. Questionnaires were given to the subjects to assess acceptability and 10 possible side effects with intensity rating at none, mild, moderate or severe. An endoscopist blinded to the medication rated the bowel prep on a 4-level scale of excellent, good, fair or poor for overall quality of the colon prep and within each of its 5 segments. Results: Median [range] age (yr) and weight (kg) at screening was 13 [9–17], 53 [27–88], and 15 [8–18], 51 [28–109] in A and B, respectively. Mean weight loss of 0.88 and 1.05, SD ± 1.04 kg for A and B, respectively was not significantly different between groups. The mean increase in serum magnesium (mEq/L) was −0.01 vs 0.14 (p=0.001), and the mean increase in serum phosphorus (mg/dL) was 0.40 vs 0.33 (p=NS) in A vs B, respectively. No statistically significant difference was observed in other electrolytes between both groups. There were no serious adverse events reported from both regimens. The side effects were not statistically significant between both regimens, apart from higher nausea intensity in regimen A (p=0.012). Bowel cleansing was similar between the groups; 71% were rated excellent or good. Willingness to repeat the prep was higher in A vs B (77% vs 32%, p<0.006). Ten subjects in regimen A had prior colonoscopies using regimen B; 9 rated A better, 1 rated A the same. Conclusion: Oral NaP is safe and effective for bowel cleansing prior to colonoscopy in children and adolescents. It has a shorter prep time, comparable side effects and is more acceptable than our standard magnesium citrate regimen.