The expedition's goal as stated by President Jefferson was "to explore the Missouri River, & such principal stream of it as, by its course & communication with the water of the Pacific ocean may offer the most direct & practicable water communication across this continent, for the purposes of commerce." In addition, the expedition was to learn more about the Northwest's natural resources, inhabitants, and possibilities for settlement,
Jefferson's instruction to Lewis were:
"Beginning at the mouth of the Missouri, you will take observations of latitude and longitude at all remarkable points on the river, & especially at the mouths of rivers, at rapids, at islands & other places & objects distinguished by such natural marks & characters of a durable kind, as that they may with certainty be recognized hereafter....The variations of the compass too, in different places should be noticed."
(considering the Native Americans) "...You will therefore endeavor to make yourself acquainted, as far as diligent pursuit of your journey shall admit with the names of the nations & their numbers, the extent & limits of their possessions; their relations with other tribes or nations; their language, traditions, monuments, their ordinary occupations in agriculture, fishing, hunting, war, arts & the implements for these, their food, clothing, & domestic accommodations, the diseases prevalent among them, & the remedies they use, moral and physical circumstance which distinguish them from the tribes they know, particularities in their laws, customs & dispositions, and articles of commerce they may need or furnish & to what extent."
"Other objects worthy of notice will be the soil & face of the country, it's growth & vegetable productions, especially those not of the US; the animals of the country generally & especially those not known in the US; the remains & accounts of any which may be deemed rare or extinct; the mineral productions of every kind, but more particularly metals, limestone, pit coal & saltpetre, salines & mineral waters, noting the temperature of the last & such circumstances as may indicate their character; volcanic appearances; climate as characterized by the thermometer, by the proportion of rainy, cloudy & clear days, by lightening, hail, snow, ice, by the access & recess of frost, by the winds, prevailing at different seasons & the dates at which particular plants put forth or lose their flower or leaf, times of appearance of particular birds, reptiles or insects."