Introduction Giardia has a wide range of host species and is a common cause of diarrheal disease in humans and animals. Molecular data have defined seven genetic assemblages of Giardia duodenalis, named A-G. Humans are infected with assemblages A and B, dogs primarily with C and D, but dogs can also be infected with assemblages A and B, and are able to transmit these zoonotic assemblages to their owners. The epidemiology and clinical impact of infections with this parasite in dogs is still not completely understood due to variable results across different studies. The aim of this study was to analyze giardia assemblage prevalence in dogs and influence of giardia assemblage on clinical symptoms and its intensity. The aim of this study was also to analyze whether co-invasion of different giardia assemblages with other parasites/pathogens has influence on clinical symptoms and its intensity. Materials and methods This research included 82 dogs (older than one year) that were admitted to the Clinic for Internal Medicine, University of Zagreb. The dogs were symptomatic (n=42) and asymptomatic (n=40). All fecal samples were examined for intestinal parasites by direct microscopic examination after the flotation technique and by immunofluorescence, and giardia positive samples were subjected to further genetic characterization by using PCR of small subunit ribosomal DNA (Ssu rRNA gene) genes. Stool samples were examined for the presence of C. perfringens by fecal culture in 5% sheep blood agar. Data on clinical symptoms, blood hematology and biochemistry were collected from the database of the Clinic for Internal Medicine, and a scoring system for the intensity of 12 gastrointestinal symptoms was constructed. Statistical analysis was done by Stata 13.1 (Stat Corp. USA). Results Prevalence rates for giardia were 30.4% (25/82) in all dogs: 30% in asymptomatic dogs, and 31% in symptomatic dogs. Giardia was more prevalent in younger animals, and there was no sex predisposition for giardia infection. Ten dogs were molecularly positive for G. duodenalis assemblage C, and 15 dogs were positive for G. duodenalis assemblage D. Zoonotic assemblages A or B were not found. The following parasites/pathogens were found: Giardia duodenalis (30.4%), Trichuris vulpis (9.76%), Cryptosporidium spp (12.19%), Isospora canis (4.88%), Ancylostoma spp/Uncinaria spp (2.44%); Toxocara canis (7.32%), Toxascaris leonina (1.21%); Clostridium perfringens (70.73%). Co-invasion of two or more parasites/pathogens was found in 35.9% of dogs with diarrhea, and giardia positive dogs were more often infected with Cryptosporidium spp than giardia negative dogs. There was no correlation between the presence of giardia or its different assemblage and the intensity and appearance of gastrointestinal symptoms in dogs, with the exception of symptoms duration: giardia positive dogs had chronic symptoms more often than giardia negative dogs. Statistically relevant co-invasion of giardia and cryptosporidium was found. Statistically important differences in concentration of BUN and activity of lipase, CPK and ALT were found in giardia positive dogs. Discussion/conclusions Almost the same prevalence of giardia in symptomatic and asymptomatic dogs shows the need to test all dogs for giardia, and also to perform treatment on all positive dogs. In our research we found only host adapted assemblages C and D with the explanation being that host adapted assemblages replicate faster and “push out” other assemblages. The offered hypothesis is that transmission of host adapted species may be favored by intensive contact between animals and that these prevail over other non-host adapted species. VII Although some research of human giardiasis showed correlation between giardia assemblage and intensity or appearance of gastrointestinal symptoms in humans, according to our research these models can not be translated to dogs. However, in this research we found only assemblages C and D, so this conclusion can not be accepted for assemblages A and B without further investigation. This study has identified an increased risk in dogs of Giardia spp. and co-infections with Cryptosporidium spp, probably due to their life cycle and contamination of same invasion reservoirs (water). From that comes the need to test all giardia positive dogs for Cryptosporidium spp.