To get an overview of the current state of endoparasite prevalences in stray and not well-cared dogs and cats, faecal samples of 445 stray and foster dogs and 837 stray and foster cats were collected at their arrival at animal shelters in Lower Saxony (Germany). They were investigated for infections with endoparasites by the use of sedimentation–flotation method. Additionally, 341 canine and 584 feline samples were investigated by IDEXX SNAP® Giardia test. Stages of endoparasites were found coproscopically in 9.4 % ( n  = 42) of the canine samples, 4.0 % were positive for Toxocara canis , 0.9 % for hookworms, 0.4 % for Toxascaris leonina and 0.2 % for Hammondia -like oocysts. Giardia -coproantigen was detected in 11.4 % of the canine samples. In cats, 33.6 % ( n  = 281) were coproscopically positive for helminths and/or protozoa. Toxocara cati was found in 27.1 %, Isospora spp. in 7.5 %, Capillaria spp. 5.0 %, Taeniidae in 2.0 %, hookworms in 1.1 %, Giardia sp. in 0.7 %, Aelurostrongylus abstrusus in 1.0 % and Toxoplasma -like oocysts in 0.1 %. Coproantigen specific for Giardia sp. was detected in 6.8 % of the feline samples. Dogs and cats up to 1 year of age were more frequently infected with endoparasites than animals over 1 year of age ( p  < 0.001). Toxocara spp. and Isospora spp. were detected significantly more often in younger dogs and cats, respectively ( p  < 0.05 and p  < 0.001). Stray dogs or cats older than 1 year were significantly more frequently infected with endoparasites than dropped off animals of the same age group ( p  < 0.05). Using the faecal egg count reduction test, the therapeutic efficacy of some anthelmintics was tested. All tested anthelmintics showed high efficacy and no suspected anthelmintic resistance was found. However, endoparasite-infected stray and free-roaming cats and dogs may contribute considerably to the contamination of public parks, playgrounds and sandpits with zoonotic parasites and therefore have to be considered a public health problem.