The geometry of milk liners may affect milking performance and cow comfort as the milk liner is the only part of the milking machine that comes into contact with the teat. To determine the effect of alternative shape of milk liners we compared square (SQR) vs. the conventional round (RND) teat cup liner on milking performance and comfort of dairy cows. Treatment milk liners were randomly allocated to clusters within each side of the 12 a side double up-herringbone dairy shed in a complete randomised block design over two periods. Milking performance data from a total of 10 065 (late stage of lactation and once-a-day milking frequency, LATE) and 18 048 (early stage of lactation and twice-a-day milking frequency, EARLY) milking events were automatically recorded by a DeLaval milk meter, and separately analysed for LATE and EARLY, respectively. In EARLY, cow comfort behaviour was also recorded during afternoon milking sessions. Across the two study periods, average milk flow rate, milk flow rate during 0–15, 15–30 and 30–60 s after cluster attachment, and milk flow rate at cluster take-off were higher in SQR compared to RND treatment. Proportion of time in a milking session with low milk flow rate and duration of milking session were less in SQR compared to RND treatment. However, effect of geometry of milk liner on peak milk flow rate was inconsistent across the two-study periods. Peak milk flow rate was higher (P < 0.001) in SQR than RND in LATE, but higher (P < 0.001) in RND than SQR in EARLY. Stomping and kicking behaviours of cows were similar between treatments. Results of this study suggest that square milk liners potentially improve milking performance, without adverse effect on cow comfort compared to conventional round liners. Long-term, multi-site studies are required to confirm potential teat-end health benefits associated with square milk liners and further verify these results.