Background In our clinic, a substantial number of patients present with transtibial residual limb pain of no specific somatic origin. Silicone liner induced tissue compression may reduce blood flow, possibly causing residual limb pain. Thus, as a first step we investigated if the liner itself has an effect on transcutaneous oxygen pressure (TcPO2). Methods Persons with unilateral transtibial amputation and residual limb pain of unknown origin were included. Medical history, including residual limb pain, was recorded, and the SF-36 administered. Resting TcPO2 levels were measured in the supine position and without a liner at 0, 10, 20 and 30 minutes using two sensors: one placed in the Transverse plane over the tip of the Tibia End (= TTE), the other placed in the Sagittal plane, distally over the Peroneal Compartment (= SPC). Measurements were repeated with specially prepared liners avoiding additional pressure due to sensor placement. Statistical analyses were performed using SPSS. Results Twenty persons (9 women, 11 men) with a mean age of 68.65 years (range 47-86 years) participated. The transtibial amputation occurred on average 43 months prior to study entry (range 3-119 months). With liner wear, both sensors measured TcPO2 levels that were significantly lower than those measured without a liner (TTE: p < 0.001; SPC: p = 0.002) after 10, 20 and 30 minutes. No significant differences were found between TcPO2 levels over time between the sensors. There were no significant associations between TcPO2 levels and pain, smoking status, age, duration of daily liner use, mobility level, and revision history.