Rapid compression machines (RCMs), as prominent zero-dimensional homogeneous reactors, have been widely applied in autoignition chemistry investigations. However, species sampling in these reactors is challenged by quantitative accuracy and the limited time allowed for transient sampling. In this study, the uncertainty of quantitative species sampling during the autoignition of a typical fuel/oxidizer mixture was numerically evaluated. Results show that the sampled species profiles tend to lag behind the "true" values due to the dilution of gases outside of the "core" region. When sampling at a longer ignition delay time, increasing the sample duration over 2 ms has very limited improvement on the sampling accuracy, and adopting a 10 mm probe tube is long enough to minimize the errors caused by dilution. In the reaction chamber where nonideal gas disturbance occurs, the sampled gases can be seriously diluted, leading to large deviations in the results. Concentration uncertainties vary among species, while uncertainties in the normalized time are consistent, which can be limited to 6% with proper piston design and sampling setups.