One of the most frequently used methods to sense breathing pattern is to detect airflow using a nasal thermistor or a thermocouple sensor. Prolonged, minimally intrusive measurement of the breathing pattern is particularly important for polysomnography, sleeping disorders, stress monitoring, biofeedback techniques, and circadian rhythm analysis. Although most applications require only breathing pattern, some applications and diagnostic procedures require monitoring of the rhythm of change of dominant nostril. In this paper we present our design of a differential thermistor-based breathing sensor for prolonged monitoring during the normal activity. The system is designed using a low power microcontroller Texas Instruments MSP430F149 with an on-chip A/D converter for data acquisition and signal processing. We use wireless RF link to a PC for long-term data acquisition and storage. Precise measurement requires decreasing zero and sensitivity errors of the measurement. We discuss signal processing methods, calibration and parameters used to characterize breathing patterns necessary for circadian breathing rhythm evaluation.