Psychophysiological science employs a large variety of signals from the human body that index the activity of the peripheral nervous system. This allows for studying interactions of psychological and physiological processes that are relevant for understanding cognition, emotion, and psychopathology. The multidimensional nature of the data and the interactions between different physiological signals represent a methodological and computational challenge. Analysis software in this domain is often limited in its coverage of the signals from different physiological systems, and therefore only partially addresses these challenges. ANSLAB (short for Autonomic Nervous System Laboratory) is an integrated software suite that supports data visualization, artifact detection, data reduction, automated processing, and statistical analysis for a large range of autonomic, respiratory, and muscular measures. Analysis modules for cardiovascular (e.g., electrocardiogram, heart rate variability, blood pressure wave, pulse wave, and impedance cardiography), electrodermal (skin conductance level and responses), respiratory (respiratory pattern, timing, and volume variables, as well as capnography), and muscular (eye-blink startle, facial and bodily electromyography) systems are complemented by specialized modules (e.g., body temperature and accelerometry, cross-spectral analysis of respiratory and cardiac measures, signal averaging, and statistical analysis) and productivity-enhancing features (batched processing, fully automatized analyses, and data management). ANSLAB also facilitates the analysis of long-term recordings from ambulatory assessment studies. The present article reviews several analysis modules included in ANSLAB and describes how these address some of the current needs and methodological challenges of psychophysiological science.