Small-animal nuclear imaging modalities have become essential tools in the development process of new drugs, diagnostic procedures, and therapies. Quantification of metabolic or physiologic parameters is based on pharmacokinetic modeling of radiotracer biodistribution, which requires the blood input function in addition to tissue images. Such measurements are challenging in small animals because of their small blood volume. In this work, we propose a microfluidic counting system to monitor rodent blood radioactivity in real time, with high efficiency and small detection volume (∼1 μL). Methods: A microfluidic channel is built directly above unpackaged p-i-n photodiodes to detect β-particles with maximum efficiency. The device is embedded in a compact system comprising dedicated electronics, shielding, and pumping unit controlled by custom firmware to enable measurements next to small-animal scanners. Data corrections required to use the input function in pharmacokinetic models were established using calibrated solutions of the most common PET and SPECT radiotracers. Sensitivity, dead time, propagation delay, dispersion, background sensitivity, and the effect of sample temperature were characterized. The system was tested for pharmacokinetic studies in mice by quantifying myocardial perfusion and oxygen consumption with 11 C-acetate (PET) and by measuring the arterial input function using 99m TcO 4 − (SPECT). Results: Sensitivity for PET isotopes reached 20%-47%, a 2-to 10-fold improvement relative to conventional catheter-based geometries. Furthermore, the system detected 99m Tc-based SPECT tracers with an efficiency of 4%, an outcome not possible through a catheter. Correction for dead time was found to be unnecessary for small-animal experiments, whereas propagation delay and dispersion within the microfluidic channel were accurately corrected. Background activity and sample temperature were shown to have no influence on measurements. Finally, the system was successfully used in animal studies. Conclusion: A fully operational microfluidic blood-counting system for preclinical pharmacokinetic studies was developed. Microfluidics enabled reliable and high-efficiency measurement of the blood concentration of most common PET and SPECT radiotracers with high temporal resolution in small blood volume. Radi onuclide-based molecular imaging using PET and SPECT is a leading diagnostic tool in oncology, cardiology, and neurology (1). In research applications, small-animal models are needed to facilitate the development of new drugs, radiotracers, and therapies that can eventually be translated to humans (2). Quantification of metabolic or physiologic disorders using radiotracer pharmacokinetic models requires dynamic blood analysis in addition to tissue imaging data (3). Whole-blood radioactivity as a function of time, the so-called arterial input function (AIF), can be extracted from PET images (4,5), using an intravascular b-microprobe (6,7) or an external blood counter connected to an artery via a catheter (8-10). Fo...