Canine intrauterine bacteriological flora during dystocia is unknown. Thus, frequency (bacterial growth (not) detected), quality (species and number of different bacterial isolates) and quantity (colony‐forming units) of intrauterine bacteria in relation to in utero foetal death in 50 bitches undergoing emergency Caesarean section were investigated. Bacterial growth was quantified from single colonies, (+) (0.5), to strong growth, +++ (3) and was observed in 34 bitches (68%), with Staph. epidermidis (n = 12), Staph. intermedius‐group (n = 7), β‐haemolytic streptococci (n = 6), Staph. aureus, α‐ and γ‐haemolytic streptococci (n = 4 each) being most common and one to four bacteria per sample. Regarding the quantity, most often (n = 46) low growth was identified. In bitches with living pups only (group I), mean number of isolates was 0.78 ± 0.83 compared to 1.60 ± 1.10 (living + stillborn pups, group II) and 1.0 ± 1.15 (stillborn pups only, group III) and mean bacterial growth in groups I/II/III was + (1.0, quantity), + (1.4) and ++ (1.6). Taking just positive samples into consideration, mean number of bacterial isolates was significantly higher in group II compared to I (p = .0088). We concluded that the canine uterus cannot be considered free of bacteria during dystocia. Mean numbers of different bacterial isolates and quantity of bacterial growth are higher in bitches with in utero foetal death.