Flies can be very irritable to cows, especially during the summer months when populations tend to be high and cows are grazing. These flies can have a negative impact on the cow’s health and production. The main objective of this study was to develop an efficient and effective way to score fly populations on cows. Cows for this study were housed on 4 organic dairy farms in the Midwest and Eastern United States. Cows were given a subjective score based on visible flies located on the side of their body that was closest to the scorer. The subjective score scale was from 0 to 4, with 0 being few to no flies and 4 being a high population of flies. Pictures were then taken of those cows to objectively count the flies. Flies were counted if they were in the region between the withers and point of shoulder back to the hip bones and down to the bottom of the barrel. Flies within this region were counted and defined as the total count for that cow. A second count of flies only on the chine was made to determine infestation levels in a smaller but more fly concentrated region. Flies were counted using the software ImageJ, which totaled and marked the flies in an image as the user clicked on them. Statistics were calculated using PROC MEANS and PROC CORR in SAS 9.4. In total, there were 144 pairs of observations of subjective scores and objective counts with 15, 51, 24, 8, and 2 percent of scores assigned as 0, 1, 2, 3, and 4, respectively. In the chine region, the mean (±SD) count of flies was 2.6 (4.7), 13.8 (16.0), 39.8 (44.7), 69.0 (57.9), and 178.0 (81.9) for scores assigned as 0, 1, 2, 3, and 4, respectively. Mean total counts for scores of 0 to 4 were 17.4 (35.0), 37.5 (36.8), 106.4 (61.9), 217.5 (94.3), and 419.3 (164.0), respectively. In order of ascending subjective score, median fly counts in the chine region were 2, 10, 23, 70, 198, and in total were 9, 26, 83, 216, and 378. On average, 35.7% of the total flies were located in the chine region and the rank correlation between chine and total side counts was 0.66 (P < 0.01). In conclusion, the subjective scores recorded on farm accurately reflected differences in fly counts, suggesting that subjective scoring is an efficient and effective method for determining fly populations on dairy cows.