The aim of the present study was to assess the acute effects of small changes in bicycle saddle height on gross efficiency (GE) and lower-limb kinematics. Well-trained cyclists (n = 14) performed a submaximal pedaling test (~70-75% of the v[Combining Dot Above]O2max) at constant cadence (90 rpm). It consisted of 3 randomized sets of 6 minutes with the preferred saddle height, 2% higher and 2% lower. Gross efficiency was significantly lower and oxygen consumption (v[Combining Dot Above]O2) was significantly higher when raising the saddle (GE = 19.9 ± 1.5%; V[Combining Dot Above]O2max = 43.8 ml·kg·min) than when lowering it (GE = 20.4 ± 1.3%; V[Combining Dot Above]O2 = 42.8 ml·kg·min). Additionally, a change of 0.8% in GE (20.6 ± 1.6% to 19.8 ± 1.6%, p < 0.05) was observed when comparing the positions where the best and worst GE was obtained. A significant effect of the small changes in saddle height on lower limb kinematics was also observed (p < 0.05). The differences between lower and higher saddle positions, in hip, knee, and ankle joints were an increase of extension (~4, 7, and 8°, respectively), a decrease of flexion (~3, 4, and 4°, respectively) and, consequently, an increase of the range of movement (~1, 3, and 4°, respectively). The results of the present study indicate that small changes in saddle height affected GE and lower limb kinematics The observed changes in lower limb kinematics could justify, in part, the GE changes. Further research should evaluate long-term effects of these small modifications in the seat height on GE and lower limb kinematics.