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Introduction: The effectiveness of colonoscopy depends on multiple factors, being two of the most important ones an adequate bowel preparation and the patient’s tolerability to the preparation. Objectives: Compare effectiveness and tolerability of two bowel preparation agents, polyethylene glycol (PEG) and sodium picosulfate/magnesium citrate (SPMC). Patients and Methods: Randomized clinical trial on outpatients that went into colonoscopy in INDISA Clinic. We evaluated effectiveness and tolerability with Boston Bowel Preparation Score (BBPS) and Lawrence questionnaire [composed by Likert scale, two qualitative questions and Visual Analogue Scale (VAS) for pain], respectively. Results: 189 patients, 123 were randomized to PEG and 66 to SPMC. BBPS average in patients in the PEG branch was 7.51 (SD 1.66) and for SPMC 7.12 (SD 1.71) (p = 0.111). Likert scale for evaluating tolerability average for PEG was 0.94 (SD 0.68) and for SPMC 0.63 (SD 0.61) (p = 0.0004). VAS scale for PEG had an average of 7.68 (SD 2.4) and for PSCM 9.04 (SD 1.59) (p < 0.0001). When we asked for workplace absenteeism, there were no significant differences between both groups and when we asked about using the same intestinal preparation in a future colonoscopy there was statistical significance in favor to SPMC (p = 0.026). Conclusions: No differences were noted on effectiveness between the PEG and SPMC bowel preparations. Nevertheless, SPMC appeared to be better tolerated by patients.