Background Kohat district is one of the low to medium intensity malaria transmission areas in Pakistan where asymptomatic carriers are likely to form a reservoir of infection. This study was done to explore the possibility of using microscopy, rapid device testing (RDT), low-cost in house real time polymerase chain reaction (RT-PCR) and End point fluorometry (EPF) for detection of malaria in the asymptomatic immediate family members of patients of malaria (homestead) and in a sample from the general population of Kohat. Objectives 1. To evaluate the feasibility of screening of malaria by polymerase chain reaction (PCR) targeting the 18S Small Subunit ribosomal RNA gene (SSUrRNA gene) in the diagnosed patients of malaria. 2. To evaluate the usefulness of PCR for SSUrRNA gene of malaria parasite in detection of suspected asymptomatic carriers of malaria. Materials and Methods This cross-sectional study was carried out at Combined Military Hospital Kohat and Molecular Lab of Riphah International University, Islamabad from Jan - Dec 2015. A total of 1000 individuals including 200 microscopy positive patients of malaria, 400 asymptomatic immediate family members (homestead) of the symptomatic patients of malaria and 400 apparently healthy controls were tested by microscopy, RDT and RT-PCR and RT- PCR followed by EPF. Results In the 200 microscopy positive patients of malaria 190 (95%) were positive by RDT and all were positive by RT-PCR. In the 400 individuals from the homestead of patients of malaria six (1.5%) individuals showed malarial parasite on microscopy, RDT failed to pick any individual with malaria and 32 (8%) were positive for malaria on RT-PCR. On fluorometry all of the RT-PCR positive results were positive and the negative results were negative. The difference in the frequency of malaria in the homestead versus general population was very significant (p = 0.0002) and the relative risk of malaria was 4.0 times higher (95% CI: 1.87 to 8.57). Conclusion The chances of detecting asymptomatic carriers of malaria is significantly higher in the homestead of malaria patients than in the general population and for this purpose low cost RT-PCR with End Point Fluorometry can be very useful in the diagnosis of malaria especially with low parasitemia.