The Agricultural technology system (ATS), which, in Nigeria, is called the Research-Extension-Farmer-Input Linkage System [REFILS] comprises individuals who are expected to interact and effectively perform activities geared towards generation, dissemination, supply and use of innovations to achieve food security and poverty alleviation. However, the impact of the system is far below expectation due to challenges experienced by components of the linkage system. This study therefore assessed research and extension practitioners' perception of the component-wise challenges and effectiveness of Nigeria's REFILS. The seventy two (72) high calibre research and extension practitioners who participated in the National Extension Planning Review Meeting (NEPRM) for 2010 constituted the respondents. Findings show that practitioners were mostly males (75%), mean age=50.1 years, years of experience (X =21.3years) and 75% had post graduate degrees. The study also revealed weak perception of linkage effectiveness (grand X =2.016) with report writing (X =2.671), management interactions (X =2.522), policy formulation (X =2.387), as activities with strongest linkage effectiveness. Linkage effectiveness scores were weak in activities such as mass media communication (X =1.298), link with input and service providers (X =1.314), liaison services (X =1.429) and joint programme implementation reviews (X =1.462). Furthermore, analysis showed significant relationships between sex (r=-0.690), educational qualification (r=0.598) and years of working experience (r=0.506). Component-wise, most serious challenges (≥50% indication) to REFILS effectiveness include poor motivation, inadequate and erratic funding, dearth of capacity building opportunities, inadequate capital for farmers, absence of strong farmers' organizations, poor participation of input agencies and poor coordination. The study concludes that practitioners were weak in linkage effectiveness, especially in field level activities due to various component-wise challenges. The study recommends improved funding support and involvement of relevant stakeholders, especially farmers' organizations and input agencies in REFILS activities by government, private and donor agencies to enhance food security in Nigeria and by extension Africa.