Compost bedded pack barn type is an alternative housing system for dairy cows and fairly new design for Turkish dairy farmers. The objective of this study was to determine the effect of hygiene score on somatic cell scores of lactating Holstein cows reared in a compost bedded pack barn system in Turkey. A total of 8,438 records of 1,068 lactating Holstein cows were used for this study. Milk samples were collected fortnighly from the cows to determine SCC, fat, lactose, protein, nonfat solids, total solids, casein, urea, freezing point, density and acidity in milk. Cow hygiene was measured using a 4-point scoring system (very clean, clean, dirty, and very dirty) for 3 different areas of the cow's body (leg, flank, and udder) and combining these scores to generate a composite cleanliness score. Hygiene score of different body parts of each cow were recorded on the day of milk sampling. Milk composition, SCS, and milk yield data were analyzed with using PROC MIXED model of SAS. The effects of parity (1–6), stage of lactation (early, mid and late lactation), season (spring, summer, autumn, and winter), year (2014, 2015), level of milk production (high and low) and hygiene score were determined as the fixed effects and the effect of cow within each hygiene score was included as a random factor in the model. Results showed that only leg (P < 0.01) and udder (P < 0.001) hygiene scores were significantly changed the somatic cell score. On the other hand, the effects of parity (P < 0.001), level of milk production (P < 0.001), stage of lactation (P < 0.001) and season (P < 0.001) were also significant on somatic cell score of cows reared in compost bedded pack barn. In conclusion, leg and udder hygiene scores were significantly associated with SCS and also during the summer months, high producing dairy cows had highest SCS especially when they are in early stage of lactation.