Fluorescence fluctuation spectroscopy utilizes the signal fluctuations of single molecules for studying biological processes. Information about the biological system is extracted from the raw data by statistical methods such as used in fluctuation correlation spectroscopy or photon counting histogram (PCH) analysis. Since detectors are never ideal, it is crucial to understand the influence of photodetectors on signal statistics to correctly interpret the experimental data. Here we focus on the effects of afterpulsing and detector dead-time on PCH statistics. We determine the dead-time and afterpulse probability for our detectors experimentally and show that afterpulsing can be neglected for most experiments. Dead-time effects on the PCH are concentration-dependent and become significant when more than one molecule is present in the excitation volume. We develop a new PCH theory that includes dead-time effects and verify it experimentally. Additionally, we derive a simple analytical expression that accurately predicts the effect of dead-time on the molecular brightness. Corrections for non-ideal detector effects extend the useful concentration range of PCH experiments and are crucial for the interpretation of titration and dilution experiments.