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Introduction In March 2014, a specialized Pilonidal Care Clinic was started at Boston Children's Hospital to standardize care; evaluate predictors of pilonidal treatment success/failure; decrease morbidity; and improve outcomes, including recurrences and quality of life. Methods A staging system for pilonidal disease was developed. Patients were treated with shaving and improved hygiene until inflammation and drainage subsided, then underwent pit-picking under local anesthesia and/or laser epilation, and followed for recurrences. Results In bivariate analysis, mild disease severity, longer duration of care in Pilonidal Care Clinic, undergoing pit-picking procedure, and female gender were statistically significant predictors of treatment success. Using multivariate regression analysis, we found that laser epilation independently led to statistically significant disease resolution. To date, the provider team (physician, physician assistant, and registered nurse) have performed >400 laser procedures without a single adverse event—establishing laser epilation as a safe, easy, and effective procedure to utilize in the treatment of pilonidal disease. Analyzing the initial 58 patients who underwent pit picking, only six patients required intraoperative treatment. Of patients with complete follow-up (n = 51), 47 (92%) were symptom- and recurrence-free for an average of 5 months without requiring narcotics or experiencing postoperative morbidity. Conclusion Minimally invasive pilonidal care with pit picking and/or laser epilation is an effective, safe, and well-tolerated treatment approach offering lower recurrence rates with minimal morbidity and avoidance of major operations.