Analysis of milk BHB concentration by Fourier-transform infrared (FTIR) spectrometry more frequently than regular milk testing could help dairy producers in decision making, particularly if it would be possible to use small hand-stripped samples (hereinafter simply called samples) taken between dairy herd improvement (DHI) test-samples analysed using DHI algorithms. The aim of this Research Communication was to evaluate milk BHB concentration and the prevalence of elevated milk BHB concentration analysed by FTIR spectrometry compared with flow-injection analysis (SKALAR) from samples taken at different times relative to the milking. A total of 293 early-lactation cows in 44 commercial dairy herds were involved in the study. Herds were visited once during the morning milking when a routine DHI test-sample was obtained using in-line milk samplers. Additional milk samples were taken by hand stripping as follows: (1) Just before connecting the milking machine; (2) immediately after removing the milking machine; (3) 3 h after milking and (4) 6 h after milking. Milk samples were analysed for BHB concentration by FTIR and SKALAR, the latter being the reference method. Milk BHB concentration from samples taken before milking was different between FTIR and SKALAR whereas no difference was noted for other sampling times, although milk BHB concentration rose as time after milking increased. Except for DHI test-samples for which prevalence was not different between analysis methods, prevalence of elevated milk BHB concentration (≥0.15 mmol/l) was greater for FTIR analysis. However, no difference in prevalence was observed between SKALAR and FTIR when using a threshold of ≥0.20 mmol/l. In summary, hand-stripped milk samples taken any time after removing the milking machine until 6 h after the milking can be recommended for FTIR analysis of elevated milk BHB concentration prevalence provided a threshold of 0.20 mmol/l is used.