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Less invasive protocols are necessary to study energy expenditure (EE) of cats living in homes for expressing their normal living conditions. The present study compared sampling times and the use of saliva, urine and blood to measure 2H and 18O to apply the doubly labelled water method. In the first study, four cats were used to evaluate the enrichment (2, 4, 6, 7 and 8 h) and elimination (2, 4, 6, 8, 10, 12, 14, 16, 18 and 20 d) of 2H and 18O (subcutaneously injected). The maximum enrichment was after 5 h (R2 0·82) of injection, with an Ln linear elimination of both isotopes (P < 0·001; R2 0·99). The results of EE were similar, regardless of the sampling time used (P = 0·999). In the second study, seven male cats and seven female cats were used. Before and after isotope injection (5 h, 7 d, 10 d and 14 d), blood, saliva and urine were collected. Isotope enrichment was lower in urine (P < 0·05) and at the similar level in blood and saliva. Isotope elimination was similar for all fluids (P < 0·473). The EE calculated with blood and saliva was similar but higher for urine (P = 0·015). According to Bland-Altman statistics, blood and saliva presented low bias and high correlation (P < 0·001), but this was not observed for urine (P = 0·096). Higher EE was observed for male cats (384 (se 39) kJ/kg0·67 per d) than for female cats (337 (se 34) kJ/kg0·67 per d; P < 0·05). The sampling time for the method is flexible, and saliva can be used as a substitute for blood.