During the puerperium, pregnancy-associated changes of the uterus need to be reversed. The duration of this process is of importance in terms of breeding efficiency and thus monitoring and treatment of the disturbed puerperium are essential. Aim of this investigation was to identify changes over time in the cellular composition of samples from endometrium and lochia in 120 mares with different obstetrical and puerperal history. In regular examinations up to 10 days post-partum the uterine involution was assessed by transrectal palpation and ultrasound. The vagina and cervix were examined using a speculum. Mares were classified as having an undisturbed or disturbed puerperium based on history and clinical findings. Uterine cytology samples were obtained with a cytology brush and lochia were obtained by manual withdrawal. Smears were done by rolling the brush or the swab on slides. They were stained using Hemacolor®-staining. In total, 238 cytology and 150 lochia smears were examined. Endometrial cells, neutrophils, and erythrocytes were distinguished by light-microscopy. Changes in the neutrophil granulocyte count in cytology and lochia smears were determined. The correlation between the number of neutrophils in cytology and lochia smears was not significant (p = 0.22). There was a significant influence of the puerperium on the percentage of neutrophils in the cytology samples (p = 0.001) but not in the lochia smears (p = 0.83). A significant decline of erythrocytes was detected in cytologies (p < 0.0001) and lochia smears (p = 0.12) of mares after eutocia but not after dystocia. Retention of fetal membranes (p = 0.0004) and time (p = 0.0034) had a significant influence on the percentage of neutrophils in the endometrial cytology. The type of birth (p = 0.0018) and the time (p = 0.0011) significantly affected the decrease in neutrophils in the cytology samples but not in the lochia smears. The influence of time was also found for the decrease of erythrocytes in cytology (p < 0.0001) and lochia (p = 0.0082) samples. A constant decline in neutrophils (p < 0.001) was found in the cytologies of mares with an undisturbed puerperium. Therefore, endometrial cytology seems to be more appropriate than lochia assessment for the evaluation of puerperal development in mares.