The toxicity of needle-(nHA-ND) and rod-shaped (nHA-RD) hydroxyapatite (HA) nanoparticles is evaluated in vitro on catfish B-cells (3B11) and catfish T-cells (28s.3) and in vivo on zebrafish embryos to determine if biological effects are similar to the effects seen in mammalian in vitro systems. Neither nHA-ND nor nHA-RD affect cell viability at concentrations of 10 to 300 μg mL−1. However, 30 μg mL−1 needle-shaped nHA lower metabolic activity of the cells. Axial deformations are seen in zebrafish exposed to 300 μg mL−1 needle shaped nHA after 120 h. For the first time, nHA is reported to cause zebrafish hatching delay. The lowest concentration (3 μg mL−1) of both types of nHA cause the highest hatching inhibition and needle-shaped nHA exposed zebrafish exhibit the lowest hatch at 72 h post fertilization.