To determine amino acid (AA) requirements for pigs in precision feeding systems, it is important to understand the sources of variation in protein utilisation among pigs. It is possible that using fixed AA ratios to determine requirements limits protein deposition (PD) and contributes to this variation. This study aimed to measure PD in pigs fed with daily tailored diets where either dietary lysine (Lys) or threonine (Thr) were provided at independent variable rates. A total of 95 growing pigs (35 kg body weight (BW)) were used, with electronic ear tags granting them access to automatic feeders. Pigs were randomly assigned to treatments according to an unbalanced 5×5 factorial arrangement with Lys and Thr provided at 5 levels (i.e. 60, 80, 100, 120 and 140% of their estimated individual requirements of Lys and Thr). The pig was considered the experimental unit and the trial lasted 21 days. Daily standardised ileal digestible Lys and SID Thr requirements were estimated using individual daily feed intake and weekly body weight measurements. Total body fat and lean content were measured by dual-energy X-ray absorptiometry on days 1 and 21. Data were analysed using a mixed regression model and means compared by a Tukey test. The variation in the response in PD to Lys and Thr observed was large and similar to those studies using fixed AA ratios, with Lys and Thr intake explaining only 11% of the variation. Results were also analysed by cluster analysis discriminating pigs with low (167 g/d, n=16), medium (191 g/d, n=38) and high (213 g/d, n=37) PD, but with same average Lys and Thr intake among clusters. Low, medium, and high PD clusters differed (P<0.05) in gain:feed ratio (0.51, 0.56, and 0.62, respectively), nitrogen retention (50, 58, and 64%, respectively), and in efficiency of Lys (71, 74 and 81%, respectively) and Thr (59, 64 and 70%, respectively) utilisation above maintenance. The efficiency of Lys and Thr utilisation decreased considerably with increasing AA intake level (P<0.001), independent of the cluster. Differences in PD were associated to differences in efficiency of nutrient utilisation, and providing Lys and Thr in an independent way did decrease the variability in PD.