This paper presents an analysis of the scientific output and collaboration of Brazilian agricultural research in the Web of Science (WoS) during 2000-2011. A total of 45,163 documents were retrieved. Data analysis was conducted with the use of the softwares Bibexcel and Pajek. The results indicated that the number of Brazilian articles in the field of agricultural sciences indexed in WoS has increased by 344%; however, the main driver for this growth was the raise in the number of national journals indexed in the database. Although Brazilian articles have been found in 799 journals from 46 countries, 53.5% of the total production was published in national journals with low impact factor. The percentage of articles with multiple authors in the total volume of publications increased from 96.1% in 2000 to 98.4% in 2011. The proportion of articles in collaboration between institutions rose from 47.3%, in 2000, to 64.2%, in 2011. However, there was a decrease in publications with international collaboration from 21.7 % in 2000 to 15.4 % in 2011. The most important collaborative relationships were established with the U.S., France and Germany.