The question of the nature of the dark matter in the Universe remains one of the most outstanding unsolved problems in basic science. One of the best motivated particle physics candidates is the lightest supersymmetric particle, assumed to be the lightest neutralino -a linear combination of the supersymmetric partners of the photon, the Z boson and neutral scalar Higgs particles. Here we describe DarkSUSY, a publicly-available advanced numerical package for neutralino dark matter calculations. In DarkSUSY one can compute the neutralino density in the Universe today using precision methods which include resonances, pair production thresholds and coannihilations. Masses and mixings of supersymmetric particles can be computed within DarkSUSY or with the help of external programs such as FeynHiggs, ISASUGRA and SUSPECT. Accelerator bounds can be checked to identify viable dark matter candidates. DarkSUSY also computes a large variety of astrophysical signals from neutralino dark matter, such as direct detection in low-background counting experiments and indirect detection through antiprotons, antideuterons, gamma-rays and positrons from the Galactic halo or high-energy neutrinos from the center of the Earth or of the Sun. Here we describe the physics behind the package. A detailed manual will be provided with the computer package.