The Cow’s Milk-related Symptom Score (CoMiSSTM) was created as an awareness tool for cow’s milk allergy. The aim of the present study was to analyze the inter-rater variability between a pediatrician, parents, and day to day variability. A Health Care Professional (HCP) and parent filled in the CoMiSS independently and blinded for each other to evaluate inter-rater variability. In order to validate day-to-day variability, a parent filled in the CoMiSS during 3 consecutive days and was compared to the CoMiSS scored by the HCP. The absolute agreement between parent and HCP was 75%, and 92.6% and 100% with a tolerance of 0, 1, and 2 points, respectively, resulting in excellent agreement with an intraclass correlation coefficient (ICC) 0.981 (95% Confidence Interval 0.974–0.986, p < 0.001). Day-to-day variability during 3 consecutive days resulted in an absolute agreement of 30%, increasing to 80% and 88.6% when 2 and 3 points, respectively, were accepted. The ICC was excellent for the parental prospective scores (0.93, 95% CI 0.90–0.96; p < 0.001). Day-to-day variability indicates that CoMiSS has a moderate inter-rater reliability. A very low variability was observed when scored prospectively over three days. Data suggest that the CoMiSS can reliably be scored by parents without additional training.