Given a polarised abelian variety over a number field, we provide totally explicit upper bounds for the cardinality of the rational points whose Néron-Tate height is less than a small threshold. These imply new estimates for the number of torsion points as well as the minimal height of a non-torsion point. Our bounds involve the Faltings height and dimension of the abelian variety together with the degrees of the polarisation and the number field but we also get a stronger statement where we use certain successive minima associated to the period lattice at a fixed archimedean place, in the spirit of a result of David for elliptic curves.