Bone anchored markers using intracortical bone pins are one of the few available methods for analyzing skeletal motion during human gait in-vivo without errors induced by soft tissue artifacts. However, bone anchored markers require local anesthesia and may alter the motor control and motor output during gait. The purpose of this study was to examine the effect of local anesthesia and the use of bone anchored markers on typical gait analysis variables. Five subjects were analyzed in two different gait analysis sessions. In the first session, a protocol with skin markers was used. In the second session, bone anchored markers were added after local anesthesia was applied. For both sessions, three dimensional infrared kinematics of the calcaneus and tibia segments, ground reaction forces, and plantar pressure data were collected. 95% confidence intervals and boxplots were used to compare protocols and assess the data distribution and data variability for each subject. Although considerable variation was found between subjects, within-subject comparison of the two protocols revealed non-systematic effects on the target variables. Two of the five subjects walked at reduced gait speed during the bone pin session, which explained the between-session differences found in kinetic and kinematic variables. The remaining three subjects did not systematically alter their gait pattern between the two sessions. Results support the hypothesis that local anesthesia and the presence of bone pins still allow a valid gait pattern to be analyzed.