Momentary time sampling (MTS), whole interval recording (WIR), and partial interval recording (PIR) are commonly used in applied research. We discuss potential difficulties with analyzing data when these systems are used and present results from a pilot simulation study designed to determine the extent to which these issues are likely to be problematic in the context of single case design studies. Results indicate that WIR and PIR may result in invalid effect size estimations. Although MTS more closely paralleled actual duration, it may induce variability in relatively short sessions, increasing the likelihood of Type II errors. Suggestions for practitioners, consumers, and researchers include careful use and reporting of data collected using interval-based systems and continued investigation of properties of these systems, particularly on the effects on effect size estimations.