How to set all the values of an existing Pandas DataFrame to zero?

The absolute fastest way, which also preserves dtypes, is the following:

for col in df.columns:
    df[col].values[:] = 0

This directly writes to the underlying numpy array of each column. I doubt any other method will be faster than this, as this allocates no additional storage and doesn’t pass through pandas’s dtype handling. You can also use np.issubdtype to only zero out numeric columns. This is probably what you want if you have a mixed dtype DataFrame, but of course it’s not necessary if your DataFrame is already entirely numeric.

for col in df.columns:
    if np.issubdtype(df[col].dtype, np.number):
        df[col].values[:] = 0

For small DataFrames, the subtype check is somewhat costly. However, the cost of zeroing a non-numeric column is substantial, so if you’re not sure whether your DataFrame is entirely numeric, you should probably include the issubdtype check.

---

Timing comparisons

Setup

import pandas as pd
import numpy as np

def make_df(n, only_numeric):
    series = [
        pd.Series(range(n), name="int", dtype=int),
        pd.Series(range(n), name="float", dtype=float),
    ]
    if only_numeric:
        series.extend(
            [
                pd.Series(range(n, 2 * n), name="int2", dtype=int),
                pd.Series(range(n, 2 * n), name="float2", dtype=float),
            ]
        )
    else:
        series.extend(
            [
                pd.date_range(start="1970-1-1", freq="T", periods=n, name="dt")
                .to_series()
                .reset_index(drop=True),
                pd.Series(
                    [chr((i % 26) + 65) for i in range(n)],
                    name="string",
                    dtype="object",
                ),
            ]
        )

    return pd.concat(series, axis=1)

>>> make_df(5, True)
   int  float  int2  float2
0    0    0.0     5     5.0
1    1    1.0     6     6.0
2    2    2.0     7     7.0
3    3    3.0     8     8.0
4    4    4.0     9     9.0

>>> make_df(5, False)
   int  float                  dt string
0    0    0.0 1970-01-01 00:00:00      A
1    1    1.0 1970-01-01 00:01:00      B
2    2    2.0 1970-01-01 00:02:00      C
3    3    3.0 1970-01-01 00:03:00      D
4    4    4.0 1970-01-01 00:04:00      E

Small DataFrame

n = 10_000                                                                                  

# Numeric df, no issubdtype check
%%timeit df = make_df(n, True)
for col in df.columns:
    df[col].values[:] = 0
36.1 µs ± 510 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)

# Numeric df, yes issubdtype check
%%timeit df = make_df(n, True)
for col in df.columns:
    if np.issubdtype(df[col].dtype, np.number):
        df[col].values[:] = 0
53 µs ± 645 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)

# Non-numeric df, no issubdtype check
%%timeit df = make_df(n, False)
for col in df.columns:
    df[col].values[:] = 0
113 µs ± 391 ns per loop (mean ± std. dev. of 7 runs, 10000 loops each)

# Non-numeric df, yes issubdtype check
%%timeit df = make_df(n, False)
for col in df.columns:
    if np.issubdtype(df[col].dtype, np.number):
        df[col].values[:] = 0
39.4 µs ± 1.91 µs per loop (mean ± std. dev. of 7 runs, 10000 loops each)

Large DataFrame

n = 10_000_000                                                                             

# Numeric df, no issubdtype check
%%timeit df = make_df(n, True)
for col in df.columns:
    df[col].values[:] = 0
38.7 ms ± 151 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

# Numeric df, yes issubdtype check
%%timeit df = make_df(n, True)
for col in df.columns:
    if np.issubdtype(df[col].dtype, np.number):
        df[col].values[:] = 0
39.1 ms ± 556 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

# Non-numeric df, no issubdtype check
%%timeit df = make_df(n, False)
for col in df.columns:
    df[col].values[:] = 0
99.5 ms ± 748 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

# Non-numeric df, yes issubdtype check
%%timeit df = make_df(n, False)
for col in df.columns:
    if np.issubdtype(df[col].dtype, np.number):
        df[col].values[:] = 0
17.8 ms ± 228 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

---

I’d previously suggested the answer below, but I now consider it harmful — it’s significantly slower than the above answers and is harder to reason about. Its only advantage is being nicer to write.

The cleanest way is to use a bare colon to reference the entire
dataframe.

df[:] = 0

Unfortunately the dtype situation is a bit fuzzy because every
column in the resulting dataframe will have the same dtype. If every
column of df was originally float, the new dtypes will still be
float. But if a single column was int or object, it seems that
the new dtypes will all be int.