Where you are likely confused is in the difference between confidence and prediction interval. Confidence intervals, which are used in geom_smooth are the predicted confidence in the estimated mean. This is a measure of how far the average of your observations will deviate at the point estimate. In predict.lm there is an option to add interval = "prediction", which would give you the prediction interval. The prediction interval incorporates the uncertainty in the error-term from y ~ x %*% beta + epsilon, while the confidence interval only incorporates the fixed effect uncertainty from y ~ x %*% beta. I have not looked into prediction intervals for loess curves, and other non- and semi-parametric smoothers, but it does not seem to be implemented in ?predict.loess We can illustrate how geom_smooth estimates the confidence intervals by manual calculation. Lets start by using the most boring reproducible example. mtcars from the stats package (included in base R). data(mtcars) fit <- loess(mpg ~ hp, data = mtcars) preds <- predict(fit, se = TRUE) names(preds) #[1] "fit" "se.fit" "residual.scale" "df" To calculate the confidence interval, we use the standard formula as you correctly specified. T <- qt(p = 0.975, df = preds$df) lwr <- preds$fit - T * preds$se.fit upr <- preds$fit + T * preds$se.fit To create a proper plot of the confidence interval i merge all the necessary info into a single data.frame, while ordering the input, to ensure proper line order. ord <- order(mtcars$hp) plotData <- data.frame(lwr = lwr[ord], upr = upr[ord], fit = preds$fit[ord], hp = mtcars$hp[ord], mpg = mtcars$mpg[ord]) Last but not least we simply need to create the plot, and compare it to the one produced by ggplot2 p1 <- ggplot(plotData, aes(x = hp, ymax = upr, ymin = lwr)) + #Data points geom_point(aes(y = mpg)) + #Line from prediction geom_line(aes(y = fit)) + #Points from prediction geom_point(aes(y = fit)) + #Confidence interval geom_ribbon(alpha = 0.3, col = "thistle1") + labs(title = "manual") p2 <- ggplot(mtcars, aes(x = hp, y = mpg)) + geom_point() + geom_smooth() + labs(title = "ggplot2") #Merge plots library(gridExtra) grid.arrange(p1, p2, ncol = 1) Now for the output: Except for some smoothing done by ggplot, and the added points for the fitted values this is easily seen to be identical. I hope this clears out how the points confidence interval is calculated.